BACKGROUND: Biventricular repair is often difficult to accomplish in patients with right atrial isomerism because of complex anomalous structures. METHODS: Ten patients with right atrial isomerism underwent biventricular repair. Their ages ranged from 15 months to 21 years. The follow-up period ranged from 1 month to 21 years. The Fontan procedure was unsuitable in 7 patients. The atrioventricular valves were separated in 5 patients and common in 5. One patient who had severe right-sided atrioventricular valvular regurgitation required concomitant prosthetic valve replacement. Another patient with a hypoplastic intraventricular septum underwent ventricular septation. Nine patients had two balanced ventricles. A ventricular septal defect was enlarged for rerouting in 3 patients. All patients had anomalous venoatrial connections and required intra-atrial baffle rerouting. One with major aortopulmonary collateral arteries underwent staged unifocalization. Three had extracardiac conduit repair. The outcomes were compared with 97 patients who underwent the Fontan procedure. RESULTS: There were 3 early deaths and 1 late death. Six survivors are in New York Heart Association functional class I or II. Two are free from medications. Two required reoperation owing to infection or prosthetic valve failure. At 1 year, cardiac index and systemic venous pressure were 3.2 +/- 0.9 L.min(-1).m(-2) and 6.6 +/- 1.6 mm Hg, respectively. There were no significant differences in survival, freedom from arrhythmia, freedom from reoperation, or exercise tolerance between biventricular repair and the Fontan procedure. CONCLUSIONS: Biventricular repair provided good long-term outcomes in patients with right atrial isomerism. In selected circumstances, biventricular repair is an acceptable alternative to the Fontan procedure.